Research in evolution and ecology of marine planktonic communities

全文

(1)

Title

Research in evolution and ecology of marine planktonic

communities

Author(s)

Blanc-Mathieu, Romain

Citation

京都大学化学研究所スーパーコンピュータシステム研究

成果報告書 (2018), 2017: 20-21

Issue Date

2018-03

URL

http://hdl.handle.net/2433/230722

Right

Type

Article

Textversion

publisher

Kyoto University

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平成

29 年度 京都大学化学研究所 スーパーコンピュータシステム 利用報告書

海洋性プランクトン群の進化と生態についての研究

Research in evolution and ecology of marine planktonic communities

Chemical Life Science Laboratory, Institute for Chemical Research, Kyoto University Blanc-Mathieu Romain

研究成果概要

My current projects are as follow:

1. Assessing the diversity and deciphering the roles of marine eukaryotic viruses in epipelagic oceans using environmental genomics and contextual data.

2. Understanding the evolutionary history of large nucleocytoplasmic DNA viruses via genomic analysis of in-lab isolated viruses.

3. Study of standing genomic variation in the phytoplankton Triparma laevis: what mechanisms shape this variation and how this variation channels future evolutionary changes?

4. Understand the processes that led to functional diversification of their phosphatidylinositol phosphate 5-kinases in core eudicotyledons.

To conduct these research projects I make use of the SuperComputer System of Institute for Chemical Research, Kyoto University. I am using various software to reconstruct phylogenies (phylobayes, RaXML, ete3 package), to assemble genomes (Spades and ABySS), to trim and map short read sequences (trimmomatic, bowtie, bwa), to perform sequence alignment and manipulation (Diamonds, Blast, Seqtk, Emboss) and to run my own scripts for parsing and downstream analysis.

発表論文(謝辞あり)

Nishimura Y, Watai H, Honda T, Mihara T, Omae K, Roux S, Blanc-Mathieu R, Yamamoto K, Hingamp P, Sako Y, Sullivan MB, Goto S, Ogata H, Yoshida T, Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean. mSphere 2,e00359-16 (2017)

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-Bhunchoth A, Blanc-Mathieu R, Mihara T, Nishimura Y, Askora A, Phironrit N, Leksomboon C, Chatchawankanphanich O, Kawasaki T, Nakano M, Fujie M, Ogata H, Yamada T., Two asian jumbo phages, ϕRSL2 and ϕRSF1, infect Ralstonia solanacearum and show common features of ϕKZ-related phages. Virology 494, 56-66 (2016)

発表論文(謝辞なし)

Carradec Q, Pelletier E, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, Lima-Mendez G, Rocha F, Tirichine L, Labadie K, Kirilovsky A, Bertrand A, Engelen S, Madoui MA, Méheust R, Poulain J, Romac S, Richter DJ, Yoshikawa G, Dimier C, Kandels-Lewis S, Picheral M, Searson S; Tara Oceans Coordinators, Jaillon O, Aury JM, Karsenti E, Sullivan MB, Sunagawa S, Bork P, Not F, Hingamp P, Raes J, Guidi L, Ogata H, de Vargas C, Iudicone D, Bowler C, Wincker P., A global ocean atlas of eukaryotic genes. Nat Commun. 9, 373 (2018)

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